Register training material
5 materials found

Keywords: BAM 

and

Authors: Obi Griffith  or blankclemens  or Martin Morgan  or Bruno Gaeta  or Yo Yehudi  or Nicolas Delhomme @delhomme 


Expression estimation

This introduces how to summarise short read alignments by the annotation of interest to obtain a count-table; i.e. the structure necessary to most downstream expression based analyses. Here, the focus is put on gene-expression, but the aspects of transcript-expression are briefly addressed.

Scientific topics: RNA-Seq

Keywords: GFF3, BAM, Populus-tremula, RNA-Seq, Expression-estimation

Expression estimation https://tess.elixir-europe.org/materials/expression-estimation This introduces how to summarise short read alignments by the annotation of interest to obtain a count-table; i.e. the structure necessary to most downstream expression based analyses. Here, the focus is put on gene-expression, but the aspects of transcript-expression are briefly addressed. RNA-Seq GFF3, BAM, Populus-tremula, RNA-Seq, Expression-estimation
Tutorial

This file describes the main tutorial PDF file. Almost all tutorials and hands-on practices are indeed collated in a single document. In addition to this PDF, R code excerpts and installation instructions are also provided.

Scientific topics: RNA-Seq

Keywords: FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, R-programming

Tutorial https://tess.elixir-europe.org/materials/tutorial This file describes the main tutorial PDF file. Almost all tutorials and hands-on practices are indeed collated in a single document. In addition to this PDF, R code excerpts and installation instructions are also provided. RNA-Seq FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, R-programming
Populus tremula shows no evidence of sexual dimorphism

**Background:** Although the majority of plant species are co-sexual, being either monoecious or hermaphroditic, a significant number are dioecious, having separate male and female individuals. Evolutionary theory suggests that males and females may develop sexually dimorphic phenotypic and...

Scientific topics: RNA-Seq

Keywords: FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression

Populus tremula shows no evidence of sexual dimorphism https://tess.elixir-europe.org/materials/populus-tremula-shows-no-evidence-of-sexual-dimorphism **Background:** Although the majority of plant species are co-sexual, being either monoecious or hermaphroditic, a significant number are dioecious, having separate male and female individuals. Evolutionary theory suggests that males and females may develop sexually dimorphic phenotypic and biochemical traits concordant with each sex having different optimal strategies of resource investment to maximise reproductive success and fitness. The establishment of such sexual dimorphism would result in changes in gene expression patterns in non-floral organs. RNA-Seq FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression
Nicolas Delhomme - Bastian Schiffthaler - October 2014 EMBO course material

Material for the course held on EBI Campus, Welcome Trust Center, Hinxton, UK on 20-26th, October 2014. The material cover general RNA-Seq data pre-processing as described in these [guidelines](http://www.epigenesys.eu/en/protocols/bio-informatics/1283-guidelines-for-rna-seq-data-analysis) and...

Scientific topics: RNA-Seq

Keywords: FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression, R-programming

Nicolas Delhomme - Bastian Schiffthaler - October 2014 EMBO course material https://tess.elixir-europe.org/materials/nicolas-delhomme-bastian-schiffthaler-october-2014-embo-course-material Material for the course held on EBI Campus, Welcome Trust Center, Hinxton, UK on 20-26th, October 2014. The material cover general RNA-Seq data pre-processing as described in these [guidelines](http://www.epigenesys.eu/en/protocols/bio-informatics/1283-guidelines-for-rna-seq-data-analysis) and reproduces the Differential Expression analysis conducted in Robinson, Delhomme et al., 2014. RNA-Seq FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression, R-programming
Alignment

Introduction to short-read alignments, including a general overview of existing methods (Burrow-Wheeler-Transform, Maximum Mappable Prefix, _etc._) and some cautionary tales.

Scientific topics: RNA-Seq

Keywords: BAM, Populus-tremula, RNA-Seq, QC, Alignment

Alignment https://tess.elixir-europe.org/materials/alignment Introduction to short-read alignments, including a general overview of existing methods (Burrow-Wheeler-Transform, Maximum Mappable Prefix, _etc._) and some cautionary tales. RNA-Seq BAM, Populus-tremula, RNA-Seq, QC, Alignment